As the size and extent of biological data sets grow, scientists turn to new quantitative techniques, such as network analysis, to understand biological complexity over large scales. For network analysis of microbial datasets, topological ‘co-occurrence’ networks are generated from correlative metrics, in which nodes represent observed variables and significant correlations are represented by the edges connecting them. We used an unprecedented decade-long time series of freshwater bacterioplankton molecular community fingerprints to test the following hypotheses: (1) community co-occurrence networks from this sample set are non-random, (2) seasonality explains the organization and complexity of co-occurrence networks, and (3) community richness and diversity correlate to co-occurrence network complexity.
Surface water samples were collected from Lake Mendota, Wisconsin, USA, and analyzed by automated ribosomal intergenic spacer analysis as described previously (Shade et al., 2007). From 2000 to 2009, a total of 34 spring, 53 summer, and 34 autumn observations were made. Thirty-two environmental variables were collected at the same location and we then quantified the richness and diversity of the underlying communities, as well as the properties of spring, summer, and autumn bacterioplankton community and biogeochemical co-occurrence networks. Using local similarity analysis, topological co-occurrence networks were generated from correlations with significant (R>0.3) local similarity scores (Ruan et al., 2006). Network comparisons were made using characteristic path length (D), and clustering coefficient (CL; Kuchaiev et al., 2011).
From spring to autumn, network complexity decreased, as indicated by decreasing CL and increasing D (Fig. 1a). The underlying communities’ richness and diversity increased (Fig. 1a) and were significantly different. Our results indicate (1) non-random bacterioplankton co-occurrence networks and (2) an inverse relationship between network complexity and diversity and richness of the underlying communities for this system. Springtime conditions were favorable to fewer taxa (lower richness), but resulted in overall more co-occurrences between taxa, especially between the most abundant taxa. Barberán et al. (2011) hypothesized that soil microbial co-occurrence network complexity was inversely related to habitat heterogeneity across broad spatial scales. In contrast, we found that network complexity was not related to heterogeneity of community habitat, as estimated by the variance of 32 physical, chemical, and biological variables across seasons, or to the complexity of co-occurrence networks of environmental variables for each season.
Correlations (edges) between temperature, day length, and dissolved oxygen and bacterial taxa were more frequent than those between taxa and other variables. Increases in bacterioplankton community diversity and richness over the open water season may be due to changes in day length, and concomitant trends in water temperature and primary productivity, which lags insolation by ~ 7 weeks in this system (Brock, 1985). Diversity and latitude are negatively related in marine bacterial communities (Fuhrman et al., 2008; Pommier et al., 2007) and putative causes of the relationship are (1) higher productivity at lower absolute latitudes accommodates greater diversity and (2) temperature controls biological process rates, including speciation. We hypothesize that in temperate regions, annual cycles in temperature and productivity control diversity of aquatic microbial communities through time, much like latitude controls diversity globally.
Brock, T. D. 1985. A Eutrophic Lake: Lake Mendota, Wisconsin (p. 308). Springer Verlag.
Fuhrman, J. a, Steele, J. a, Hewson, I., Schwalbach, M. S., Brown, M. V., Green, J. L., & Brown, J. H. (2008). A latitudinal diversity gradient in planktonic marine bacteria. Proceedings of the National Academy of Sciences of the United States of America, 105(22), 7774-8. doi:10.1073/pnas.0803070105
Pommier, T., B. Canbäck, L. Riemann, K. H. Boström, K. Simu, P. Lundberg, A. Tunlid, and A. Hagström. 2007. Global patterns of diversity and community structure in marine bacterioplankton. Molecular ecology, 16(4), 867-80. doi:10.1111/j.1365-294X.2006.03189.x